Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net	Kernel	tpr_down_ci_0.95	tpr_up_ci_0.95	fpr_down_ci_0.95	fpr_up_ci_0.95	f
biological_process	ct	0.0837887067395264	0.116575591985428	0.000367559261549628	0.000701865209760493	0.12797619047619
biological_process	el	0.0133495145631068	0.0266990291262136	0.0039606398404883	0.0111764431371956	0.00520198325611639
biological_process	ka	0.13357619914997	0.170613236187007	0.000455704657393107	0.000798353263595665	0.173853989813243
biological_process	rf	0.0837887067395264	0.117182756527019	0.000335713771746963	0.00070242573209431	0.12797619047619
cellular_component	ct	0.0697815533980582	0.100121359223301	0.000460476754617662	0.00101540627191351	0.0968506603454115
cellular_component	el	0.0333535476046089	0.0527592480291086	0.0326209040275033	0.053668329966965	0.00193923723335488
cellular_component	ka	0.0703883495145631	0.0983009708737864	0.000446983502806492	0.00116530379613624	0.0987569060773481
cellular_component	rf	0.0558252427184466	0.0849514563106796	0.000305278310040542	0.000659059390105018	0.0982286634460548
disease	ct	0.347945205479452	0.415068493150685	0.00176322682510564	0.00219777796031116	0.223871849970697
disease	el	0.178082191780822	0.218493150684931	0.00624148557834181	0.00807083512063935	0.0450617283950617
disease	ka	0.289041095890411	0.358921232876712	0.000415552452488082	0.000663219827992711	0.3674228337672
disease	rf	0.346575342465753	0.407534246575342	0.00169937056405857	0.00216133212861302	0.225273631840796
gene_PS	ct	0.155490767735666	0.224514091350826	0.000802150365533896	0.00125218308234751	0.193849021435228
gene_PS	ka	0.399805447470817	0.470817120622568	0.000922636812641577	0.00150829076228692	0.354312354312354
gene_PS	rf	0.32295719844358	0.406639105058366	0.00104034661901471	0.00137551711346651	0.304783950617284
gene_TF	ct	0.0285714285714286	0.114285714285714	0.0307697983275947	0.10315324916653	0.00516929439131559
gene_TF	el	0	0.0214285714285714	0.0025031425916817	0.035098923320763	0.00505050505050505
gene_TF	ka	0.0357142857142857	0.128571428571429	0.0440277094605673	1	0.00450704225352113
gene_TF	rf	0.0928571428571429	0.214285714285714	0.0637161829808165	0.175386402142428	0.00600272851296044
gene_hgncGroup	ct	0.0839469808541973	0.117083946980854	0.00104135722411007	0.00171589534095602	0.0832589949449896
gene_hgncGroup	el	0.148857774502579	0.191599115696389	0.00126390802720085	0.00222768853396286	0.123949579831933
gene_hgncGroup	ka	0.117170228445099	0.156963890935888	0.000489382737842744	0.00116398627837923	0.158995815899582
gene_hgncGroup	rf	0.0957995578481945	0.131908621960206	0.000700819002653163	0.0011948454341623	0.113046569498756
genetic_interaction_effect_bicor	ct	0.0323785803237858	0.0516967621419676	0.000593261901954268	0.00184306090070002	0.0431519699812383
genetic_interaction_effect_bicor	el	0.00186799501867995	0.00933997509339975	0.000124888779305983	0.00261524071910209	0.00932159502848265
genetic_interaction_effect_bicor	ka	0.0330012453300125	0.0510585305105853	0.000430397285679063	0.0010603754167426	0.0520361990950226
genetic_interaction_effect_bicor	rf	0.0317559153175592	0.0529420921544209	0.000582032631883623	0.001877271314173	0.0431789737171464
molecular_function	ct	0.0538885486834048	0.0796080832823025	0.000377606681208468	0.00110542225570987	0.0825190010857763
molecular_function	el	0.00856793145654835	0.0195838433292534	0.00858204171008719	0.0223387856323128	0.00187083129982105
molecular_function	ka	0.0642988364972443	0.091855480710349	0.000613093108684663	0.00131968430150283	0.0818494220556076
molecular_function	rf	0.0545009185548071	0.0820728720146969	0.000345578838618719	0.00103322769949336	0.0861172976985895
pathway	ct	0.139356814701378	0.209800918836141	0.00144372381648818	0.00282957053914969	0.133632790567097
pathway	ka	0.193213190184049	0.273006134969325	0.000666247503387193	0.00153290744977302	0.250587314017228
pathway	rf	0.167139570552147	0.234662576687117	0.000726132039850126	0.00146430932883188	0.208269525267994
phenotype	ct	0.210277214334009	0.273833671399594	0.000623219934473963	0.000911702802727853	0.250754274220583
phenotype	el	0.0310810810810811	0.0506756756756757	0.00127507630237388	0.00260088208636739	0.0282996984458362
phenotype	ka	0.226504394861393	0.293441514536849	0.000405003006299849	0.000600665251634136	0.308575803981623
phenotype	rf	0.211629479377958	0.270453008789723	0.000615756222683856	0.000890292952174557	0.251347708894879
protein_interaction	ct	0.260216346153846	0.307091346153846	0.000956129931071146	0.00130997919568007	0.228639618138425
protein_interaction	el	0.262605168269231	0.316721754807692	0.000682552865364557	0.000944326336676263	0.280022446689113
protein_interaction	ka	0.259771497294047	0.307892363199038	0.00062831806236018	0.000964494082433261	0.272212790039615
protein_interaction	rf	0.251802884615385	0.302899639423077	0.000804131180468038	0.00106947287965815	0.244357976653696

Table 2. Performance summary for every kernel after integration

Integration	Kernel	tpr_down_ci_0.95	tpr_up_ci_0.95	fpr_down_ci_0.95	fpr_up_ci_0.95	f
integration_mean_by_presence	ct	0.187350835322196	0.23090692124105	0.000672449362725385	0.000980750962272358	0.203351320647543
integration_mean_by_presence	ka	0.324776119402985	0.373134328358209	0.000294939404058264	0.000509039764499862	0.39986399183951
integration_mean_by_presence	rf	0.256716417910448	0.307462686567164	0.000544176023939847	0.000795079692626976	0.286556603773585
mean	ct	0.245211813842482	0.292974343675418	0.000899129646195639	0.00133519136704227	0.225900681596884
mean	ka	0.352835820895522	0.427477611940298	0.000413941041869598	0.000667358107217398	0.424922118380062
mean	rf	0.285970149253731	0.341492537313433	0.000732950065989486	0.00110441983367469	0.283033620015637

Backup Pairs Coverage By Layer Non integrated

Backup Pairs Coverage By Layer Integrated

Distribution of ranks in dataset by non integrated kernels

Distribution of ranks in dataset by Integrated kernels

ROC-AUCs for Non-integrated kernel and layer

ROC-AUCS for integrated kernels

CDF plots of non integrated kernels

ROC plots of non integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels